Exploring the Functionality of Microbes in Fermented Foods: Technological Advancements and Future Directions

Abstract

Fermentation is a promising food processing technique that has been used throughout history for its role in food preservation, the enhancement of nutritional content, and improvement of sensory attributes. Beyond the primary probiotic benefits, microorganisms in fermented foods play a functional role in increasing nutrient bioavailability, exhibiting antimicrobial properties, producing bioactive compounds, and removing antinutritional factors. This review explores microbial diversity and its role in the production of fermented foods across different regions of the world through a dynamic market analysis. It also highlights recent biotechnological advancements in fermentation, specifically the use of omics, multi-omics, and precision fermentation. Omics technologies have been found to provide a deeper insight into microbial diversity, deciphering their metabolic pathways and functional interactions, whereas precision fermentation is being used for the manipulation of microbial processes to optimize the fermentation process and produce the desired attributes in fermented foods. Various sustainable substrates have also been used in the production of fermented foods, apart from the conventional ones. Interestingly, this review discusses the growing role of artificial intelligence, machine learning, and the Internet of Things in food fermentation, focusing on their potential to optimize processes, predict microbial interactions, and improve quality control, supported by relevant successful examples. The review also examines the current challenges faced by the fermented food industry, offering various mitigation strategies to overcome these obstacles. Possible future prospects are also explored. Through a combination of traditional methods and modern biotechnological innovations, functional fermentation is bound to transform the global food industry.

1. Introduction

Fermentation is a traditional, cost-effective, and popular food processing technique that enhances the nutritional value, digestibility, palatability, and sensory attributes of food, along with preserving the food through microbial action [1]. It has evolved on the basis of regional culinary traditions, locally available raw materials, microbial diversity, climatic conditions, and fermentation knowledge. For example, soybean-based fermented products such as Natto, Miso (Japan), Tempeh (Indonesia), and Doenjang (Korea) are widely consumed across Asia, offering probiotic and rich nutritional benefits [2]. Similarly, European countries are known for their dairy-based fermented products, such as yoghurt, Kefir, Kumiss [3], and various types of cheeses, which contribute to gut health and food preservation and act as an appetizer. Developing nations like Africa and Latin America emphasize cereal-based fermented foods such as Ogi (Nigeria), Injera (Ethiopia) [4], and Chicha (Peru), which enhance the digestibility and nutrient bioavailability of locally cultivated cereals. Apart from plant-based fermented products, meat-based fermented products are also popular, like German Salami, Portuguese Chouriço, and Thai Nham, which utilize microbial fermentation to preserve and enhance flavour. Vegetable-based ferments such as Kimchi (Korea), Sauerkraut (Germany), and pickles (India) are valued for their probiotic content and extended shelf life [5,6]. Beyond flavour and preservation, fermentation enhances functional properties, making it a key food processing technique for sustainable and health-promoting diets worldwide.

The following major question arises: what role do microorganisms play in food fermentation? The microorganisms break down complex organic molecules, such as sugars into alcohol and proteins into bioactive peptides and amino acids. This natural metabolic process in turn enhances the flavour, texture, and aroma of foods and beverages, making them more appetizing and nutritious. That is why fermented cheese and yoghurt taste far better and are healthier. Not only this, but the microorganisms in fermentation also increase the bioavailability of vitamins, boost probiotic activity, strengthen antimicrobial properties, and promote the production of antioxidants [7]. Strains such as Lactobacillus, Bacillus, Streptococcus, and Saccharomyces play a key role in vitamin production, enzymatic activity, and fibrinolytic activity, providing a natural and cost-effective alternative to synthetic food fortification [8]. In a way, fermented foods can be a viable alternative to synthetic food fortification, with minor technological advancements. Fermented foods, especially those made from soy and dairy, possess significant antioxidant and bioactive properties, which are transformed due to microbial activity and the duration of fermentation [9]. Microbial proteolysis produces bioactive peptides that support blood pressure regulation and immune function, while enzymes like amylase and protease improve digestibility and enhance functional properties. Additionally, these microorganisms help detoxify anti nutritional compounds such as phytic acid and cyanogenic glycosides, enhancing food safety and improving nutrient bioavailability [10].

The rapid expansion of the global fermented food market, valued at USD 105.8 billion in 2023, is anticipated to grow at a compound annual growth rate (CAGR) of over 6.6% between 2024 and 2032, as stated by the Global Market Insights Report, 2024 (‘Fermented Processed Food Market Size—By Product Type (Dairy Products, Bread and Bakery Products, Vegetables, Condiments, Beverages), Microorganism Type (Bacteria, Yeast, Mold), & Forecast, 2024–2032’). It is driven by an increasing consumer demand for functional and minimally processed foods. Fermented products now make up nearly one-third of the world’s food consumption, reflecting their growing significance in modern diets. However, this rising demand also raises important safety concerns, as improper fermentation techniques and inadequate hygiene can pose health risks [11]. These factors can lead to the accumulation of biogenic amines, harmful bacterial contaminants, and mycotoxins [12]. Therefore, ensuring the safety and quality of fermented products has become increasingly important, leading to the adoption of advanced technologies like high-throughput sequencing, predictive microbiology models using artificial intelligence (AI), biosensors, and PCR-based methods for detecting contamination. These innovations play a crucial role in maintaining food integrity and consumer trust and growing global demand [13]. Although fermented foods hold great cultural and nutritional value, their large-scale industrial production remains relatively limited. Overcoming these challenges requires continuous research, focused on optimizing fermentation techniques, enhancing microbial efficiency, and identifying alternative substrates beyond conventional raw materials to improve both sustainability and affordability [14]. By using advanced biotechnological techniques like omics, which basically includes genomics, transcriptomics, proteomics, and metabolomics, a better understanding of how microbes interact and function at the molecular level can be gained. Multi-omics, which combines suitable omics, is also becoming a promising technique for understanding the functional role of microorganisms in food fermentation [15]. Apart from this, recent advancements in precision fermentation are unlocking new ways to alter microbial metabolism, allowing for the targeted production of desired bioactive compounds. This process not only boosts the nutritional value of fermented foods, but also elevates their flavour, texture, and overall sensory experience, making them more appetizing and beneficial to consumers [11]. By applying these advanced biotechnological techniques, manufacturers can achieve more consistent results, enhance fermentation efficiency, and scale up production to meet the growing food industry demands [1].

This review offers a comprehensive and novel perspective on the functional roles of microorganisms in fermented foods by addressing the key questions of why, what, and how. While the nutritional and functional benefits of fermented foods are well documented, their global market analysis remains insufficiently explored, representing a significant gap in the current research. Furthermore, the application of advanced biotechnological approaches such as omics, multi-omics, and precision fermentation has yet to be fully leveraged to understand microbial functions in food fermentation. This review aims to bridge these gaps by integrating traditional knowledge with emerging biotechnological innovations. It also explores the role of AI, machine learning (ML) and the Internet of Things (IoT) in optimizing fermentation processes. In addition, key industrial challenges are critically examined alongside potential mitigation strategies and future directions. Overall, this review lays a strong foundation for advancing future research and industrial applications in microbial food fermentation, with the goal of enhancing food security, sustainability, and nutritional quality.

2. Functional Role of Microorganisms in Fermented Foods, Their Diversity Across Regions of the World, and Market Insights

Due to variations in the microbial strains employed and the availability of substrates, the functional characteristics of fermented foods differ greatly between geographical locations. Based on this, fermented food belongs to few major classes: fish products, meat products, dairy products, cereal products, vegetable products, and alcoholic beverages. The following section offers a brief overview of the key categories of fermented foods along with their respective market shares, highlighting their global significance and commercial impact.

2.1. Fermented Fish Products

Due to their historical, cultural, and environmental significance, fermented fish products are very popular throughout Asia, Africa, and parts of Europe, especially in South and Southeast Asia. Several South Asian nations, including India (particularly the northeastern states of Manipur and Tripura), Sri Lanka, Bangladesh, Bhutan, and Nepal, include fermented fish as part of their traditional diets. For example, fermented fish products like Indian Matkashidal are both economically and culturally significant [16,17]. Consuming fermented fish in the form of pastes and sauces has long been a tradition in Southeast Asian nations like Thailand, Cambodia, Vietnam, Malaysia, the Philippines, and Indonesia. In Cambodia, for example, Prohok has been subject to government regulations because of its significance to the country [18]. East Asian countries like China, Japan, and Korea also add a variety of fermented fish products to the culinary traditions of the world. For example, microbial strains like Tetragenococcus, Lentibacillus, and Carnobacterium are present in fermented Chinese fish products like Chaoshan fish sauce. The microbial activity in fish sauce fermentation significantly elevates amino acid nitrogen levels and inhibits biogenic amine formation, improving the product quality and flavour. Fish sauce is a rich source of essential amino acids, minerals, vitamins, and bioactive compounds with antihypertensive, cholesterol-lowering, and antioxidant properties, which make these fermented food products beneficial to cardiovascular health [19]. Similarly, high salt fermentation with Lactobacillus fermentum, Bacillus subtilis, and Enterococcus faecium is used in African fermented fish-based products like Lanhouin (West Africa), which improve probiotic and antioxidant activity and increase food safety by reducing biogenic amine levels [20]. Products like Rakorret (fermented trout) and Surströmming (fermented herring), as well as fermented Anchovies in France and Spain, continue to be a staple of traditional diets throughout Europe, especially in Scandinavian nations like Sweden and Norway [21]. Several reasons contribute to the popularity of fermented fish products, one of which is the need for preserving fish during times of scarcity, particularly in areas with seasonal abundance and unfavourable drying conditions, like Northeast India during the monsoon season. In regions with high humidity and little sunlight, fermentation is more practical than drying, while in economically disadvantaged areas, fermented fish is an affordable source of protein and minerals because it provides vital nutrients and complements staple foods like rice [22]. In many regions of Asia, fermented fish is still not well recognized despite its nutritional and economic importance, necessitating more research into its makeup, potential health effects, and business prospects [16]. The global fish fermentation market is dominated by Europe, which holds the largest market share of about 40% and was valued at USD 217.7 million in 2023. North America, with a USD 206.8 million valuation, comes second, with 38% of the market. In addition, the region comprising Asia and the Pacific is becoming a more lucrative and promising market due to factors like the growing population, growing health consciousness, and increased consumption of fermented fish products. According to Future Market Insights (FMIs) 2023, the Asia and Pacific market is expected to reach a valuation of over USD 98.0 million, indicating that it has the potential to grow significantly over the next few years [23].

2.2. Fermented Meat Products

Fermented meat products represent a significant segment of traditional and functional foods, offering both preservation advantages and potential health benefits. Meat fermentation, which has historically been used to improve flavour, texture, and shelf life, has changed with the introduction of probiotic starter cultures to create functional fermented meat products [24]. For example, Lactobacillus plantarum, Staphylococcus xylosus, Pediococcus pentosaceus, and Micrococcus spp. are used for the fermentation of meat products in China, including Guizhou sour meat, Sichuansausage, and Jinhua ham. These strains lead to the production of key metabolites such as esters, alcohols, acids, free amino acids (FAAs), and antioxidant peptides. They also develop flavour and suppress harmful compounds like nitrites and biogenic amines [19]. Similarly, Staphylococcus carnosus, Lactobacillus sakei, and Pediococcus acidilactici are found in fermented meats like Spanish Chorizo and Italian Salami in Europe. These microorganisms aid in immune system function, gut microbiota balance, and cholesterol metabolism [8]. The production of bioactive compounds, enzymatic activity, and probiotic composition are the main reasons for the health advantages of fermented meat and fish products. Bile salt hydrolases (BSHs), which lower cholesterol and promote cardiovascular health, are produced by lactic acid bacteria (LAB) strains like Lactobacillus curvatus [25] and Staphylococcus xylosus [26,27]. Further, fermentation improves the bioavailability of essential amino acids, omega-3 fatty acids, and vitamins, which improve gut microbiota balance, metabolic stability, and overall health [28]. Additionally, L. plantarum [29] and P. pentosaceus [30] produce antioxidant peptides that combat oxidative stress and inflammation, potentially improving cardiovascular health and immune function. The global market for fermented meat products was estimated to be at USD 149.76 billion in 2023, and is expected to grow from USD 161.78 billion in 2024 to USD 300 billion in 2032 at a CAGR of 8.02%, with the largest market share from North America (USD 24.5 billion), followed by Europe (USD 22.8 billion) in 2023 [31]. In another report, the Asia–Pacific region was found to be dominating the fermented meat market, followed closely by North America in 2024 [32]. Geographically, North America, Europe, and Asia–Pacific were the main consumption markets in 2022, and together, they accounted for the majority of the global volume sold. In conclusion, the market for fermented meat products is expanding due to both the growing global demand for convenient, tasty, and nutrient-dense meat products and technological developments in fermentation.

2.3. Fermented Dairy Products

Dairy fermentation holds an equally significant position across cultures. The microbial transformation of milk produces bioactive compounds with significant health benefits, in addition to extending its shelf life. Globally, fermented dairy-based products are an essential component of traditional diets, which are influenced by cultural customs and regional microbial diversity [8]. Cheese is one of the most popular and versatile fermented dairy products consumed across the globe, offering both traditional and probiotic options. Popular types include Gruyère and Beaufort (made with Brachybacterium alimentarium), Camembert (using Penicillium camemberti), and blue mould cheeses like Roquefort (Penicillium roqueforti). These cheeses are staples in Europe, viz. Gruyère in Switzerland and Camembert in France, while fresh cheeses like Minas (Brazil) and Cottage cheese (global) are also widely consumed [33,34]. Probiotic cheeses, such as Cheddar, Edam, and fresh cheeses, are gaining popularity for their health benefits. They contain live cultures like Lactobacillus acidophilus, Bifidobacterium, and L. rhamnosus, which support gut health, reduce cholesterol, and may even lower risks of dental caries and oral candidiasis. These bacteria survive harsh stomach conditions better in cheese than in yoghurt due to cheese’s higher fat content and dense matrix. Cheese is known to have several potent health benefits, like increased IgA antibodies and macrophage activity; bioactive peptides in cheeses like Cheddar may help manage hypertension and reduce Streptococcus mutans (linked to cavities) and oral yeast levels [35,36,37]. Similarly, Dahi, a fermented milk-like yoghurt, is popular in India, while the Himalayan regions are well known for their hardened Yak Milk Cheese, Chhurpi and Kharvas (Junnu, Posu), which are dairy products made from colostrum [20]. These food products, which are naturally fermented by Lactobacillus plantarum, Lactobacillus fermentum, and Lactococcus lactis, improve gut microbiota, increase digestibility, and generate bioactive peptides with antimicrobial and antioxidant qualities. Similarly to this, people in Russia and Mongolia have long consumed Kumiss (Koumiss) [38], a fermented mare’s milk that is high in probiotics and known to enhance lactose digestion and offer antimicrobial benefits due to the strains Kluyveromyces marxianus and Lactobacillus delbrueckii [3]. Greek yoghurt is similar to Skyr, a thick, high-protein fermented dairy product found in the Nordic nations, especially Iceland, Sweden, and Norway [39]. The predominant microbial strains in Skyr include Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus, which are responsible for the probiotics’ immune-modulating, cholesterol-lowering, and protein bioavailability-enhancing effects. Japan, which is renowned for its probiotic research breakthroughs, created the fermented milk beverage Yakult, which contains Lactobacillus casei and has become well known worldwide for its ability to improve gut health, lower inflammation, and boost immunity [40]. Amasi (Mabisi), a naturally fermented sour milk that originated in Africa, especially in the Southern and Eastern regions, is produced by native microflora such as Lactococcus lactis and Leuconostoc mesenteroides [4]. These microorganisms generate antimicrobial substances like bacteriocins, which support the balance of the gut microbiome and aid in the inhibition of harmful bacteria. A symbiotic combination of LAB and yeasts such as Lactobacillus kefiranofaciens and Saccharomyces cerevisiae is found in Kefir, a fermented milk beverage that has gained popularity in the Middle East and Turkey. These microbes have been shown to have anti-inflammatory, hypertension-lowering, and gut microbiota-enhancing properties [41]. The microbes that ferment dairy products provide a variety of useful advantages across regions, such as the synthesis of bioactive peptides, antimicrobial substances, and vital vitamins like folic acid and B₁₂ [20]. Fermented dairy products are, therefore, an essential component of both conventional and contemporary functional foods because of their health-promoting qualities, which also support immunological responses, metabolic regulation, and digestive health. Global sales of fermented dairy products are expected to grow from USD 316.33 billion in 2024 to 434.35 billion in 2030 at a CAGR of 5.51% [42].

2.4. Fermented Cereal Products

Apart from fish-, meat-, and dairy-based fermented products, cereal-based products are also prominent in many parts of the world. The Asia–Pacific region has a warm, humid climate, ranging from tropical to subtropical, which makes it ideal for growing rice paddies and supporting the growth of moulds. Because rice is a staple food and high population density limits large-scale animal farming, the region has developed unique food processing traditions, notably fermenting grains with moulds. Fermented cereal consumption across the region differs based on the local geography and climate. In the tropical areas of Southeast Asia, rice is the main grain eaten. Meanwhile, in the cooler, more temperate areas of Northeast Asia, such as Northern China, Korea, and Japan, people eat a broader variety of fermented grains, including wheat, barley, corn, millet, buckwheat, soybeans, and rice. Similarly, cereal crops, especially maize, which originally comes from Mexico, play a vital role in the diet of people in Latin America. For centuries, these grains have often been consumed in fermented forms as part of traditional food practices [43]. Regarding Africa, products like Ogi, Mawe, Kenkey, Injera, and Bushera are popular, while fermented foods made from rice and wheat, such as sourdough bread, beer, and rice wine, are more popular in Asia and Europe [44]. These foods undergo microbial fermentation primarily driven by LAB, including Lactobacillus plantarum, Lactobacillus fermentum, and Streptococcus thermophilus, alongside yeasts such as Saccharomyces cerevisiae. The microbial fermentation of cereals reduces antinutritional factors and breaks down complex nutrients, enhancing palatability, digestibility, and bioavailability. It leads to the production of organic acids, bacteriocins, and other bioactive compounds, which lower the pH and inhibit pathogens like Aspergillus flavus, thereby improving food safety and nutritional quality [45]. Additionally, by improving the protein content, improving the amino acid profiles, and raising the bioavailability of micronutrients, fermentation dramatically changes the nutritional makeup of cereals. For example, the protein content of fermented foods like Nigerian Akuma rose from 12.8% to 18.5%, and Bushera from southwestern Uganda increased from 7.79% to 11.63% [46]. Similarly, fermentation has been proven to lower carbohydrate levels because of microbial metabolism, such as Akuma’s reducing sugar content rising from 5.3% to 17.6% and its starch content decreasing from 68.1% to 37.4%, indicating improved digestibility [46]. By strengthening immune responses, decreasing gastrointestinal disorders, and encouraging healthy microbiota, these biochemical alterations also improve gut health. Foods made from fermented cereals are especially useful in sub-Saharan Africa, where they are utilized as nutrient supplements directed by the microbiota to combat childhood malnutrition, which is actually very high in Africa. They are promising functional foods because of their capacity to alter gut microbiota, improve nutrient absorption, and promote general metabolic health. Fermentation also improves mineral bioavailability by lowering antinutritional elements like tannins and phytic acid [8]. Specific details on market size and dynamics are unavailable for fermented cereal products. But the major market players in non-alcoholic cereal-based fermented drinks have been identified as North America, Europe, and Asia–Pacific [47].

2.5. Fermented Fruit, Vegetable, and Soy Products

Foods made from fermented fruits, vegetables, and soy are highly regarded for their numerous health benefits, in addition to their unique flavours. Fermented fruits like mango, wine, and pickled citrus are more common in China, India, and tropical regions, while fermented vegetables like Kimchi, Sauerkraut, and pickled cucumbers continue to be staple foods in places like Korea, Europe, and Southeast Asia, respectively [48]. These fermented foods depend on microbial consortia that promote the synthesis of bioactive compounds, particularly Lactobacillus plantarum, Pediococcus acidilactici, and Leuconostoc mesenteroides, as well as Saccharomyces cerevisiae [49]. The fermentation process supports antioxidant activity, inflammation modulation, and gut microbiome health by enriching vitamins B and C and increasing polyphenol and flavonoid contents [50]. Microbial metabolism produces short-chain fatty acids (SCFAs), like acetic and butyric acid, which are essential for intestinal health and lipid regulation. When it comes to soy-based fermentations, microbial activity can be observed, specifically of Bacillus subtilis, Aspergillus oryzae, and LAB strains, in traditional foods like Tempeh, Natto, Miso, and Soy Sauce, which are primarily produced throughout Asia [9]. While Natto, which is rich in strain Bacillus subtilis natto, produces nattokinase, an enzyme with cardiovascular benefits, Tempeh fermentation improves protein digestibility by breaking down antinutritional factors like phytic acid and trypsin inhibitors [2]. In addition, fermented soy products increase the bioavailability of isoflavones, which have been connected to a lower risk of hormone-related cancers and improved vitamin K₂ levels, which support bone health. Additionally, the balance of the gut microbiota and metabolic stability are supported by probiotic enrichment in fermented soy products like Miso and Soy Milk, especially through species like Lactobacillus helveticus and Bifidobacterium [13]. Lactobacilli and Pediococcus spp., key LABs, exhibit strong metabolic activity in fermenting vegetables and soy products by bio converting volatile compounds such as phenols, terpenes, alcohols, and aldehydes. Probiotic microbes further enhance the biosynthesis of essential metabolites including vitamins, antioxidants, and bacteriocins. These metabolites contribute to improved nutritional quality, support vital cellular functions like DNA synthesis and neuronal activity, and enhance food safety and shelf life by preserving vitamins and inhibiting spoilage organisms [49]. These fermented foods serve as functional dietary components with potential benefits for immune system support, metabolic health, and sustainable nutrition, making them more than just culinary traditions. The market for soy-based fermented products has been estimated to grow at a CAGR of 5.5%, from USD 25 billion in 2023 to USD 40 billion in 2032. The leading market drivers are Asian countries—China, Japan, and South Korea [51].

2.6. Fermented Alcoholic Beverages

Deeply ingrained in human culture, fermented alcoholic beverages have long been produced using microbial fermentation from a variety of cereals, fruits, and tubers for recreational purposes. The most classic example of this is wine. Its fermentation is driven by a mix of yeasts and LAB. Saccharomyces cerevisiae is the primary yeast used due to its high ethanol tolerance and efficiency in converting sugar to alcohol. Non-Saccharomyces yeasts like Torulaspora delbrueckii, Schizosaccharomyces pombe, and Lachancea thermotolerans enhance aroma, reduce acidity, and increase glycerol content, while others like Hanseniaspora uvarum and Pichia kluyveri boost fruity esters but require co-fermentation with S. cerevisiae. LAB such as Oenococcus oeni and Lactobacillus spp. perform malolactic fermentation, reducing wine’s acidity and improving stability. These microbes not only influence the flavour and alcohol content but also help to degrade toxins like ochratoxin A [52,53]. Globally, France, Italy, and Spain lead wine production through traditional methods, while New World regions like the USA, Australia, and South America adopt innovative approaches like Genetically Modified Organism (GMO) yeasts and micro-oxygenation [54]. Warmer climates focus on lowering ethanol, while cooler regions preserve acidity. Emerging trends include GMO yeasts for combined fermentation and sustainable practices like converting grape waste into biofuels using microbial fermentation [52]. In addition to their recreational value, these products contain bioactive compounds that, when consumed in moderation, may have health benefits. Although these drinks are frequently criticized for possible health hazards, the moderate use of them has been linked to a number of beneficial effects. For example, the abundant probiotic microorganisms like Saccharomyces cerevisiae, Pediococcus pentosaceus, and Lactobacillus plantarum are used in northeast Indian rice-based alcoholic beverages like Apong and Bhaati Jaanr [55]. They support better gut microbiota, digestive health, and metabolic regulation. Similarly, red wine and traditional rice wines, which are fermented beverages rich in polyphenols, contain bioactive compounds that have anti-inflammatory, antioxidant, and cardioprotective qualities. These compounds lower the risk of cardiovascular diseases and improve lipid metabolism [56]. According to studies, the polyphenols found in wine and beer may improve endothelial function, lower low-density lipid (LDL) cholesterol, and lessen oxidative stress, all of which may improve heart health. Furthermore, native millet-based fermented beverages and beer, which are popular in Africa and some parts of Asia, contain organic acids and phytochemicals that have been demonstrated to support immune function and control blood sugar levels [57]. By regulating the intestinal microbiota and suppressing harmful bacteria, the metabolic by-products of yeast and LAB in these drinks improve gut health, in addition to adding flavour and aroma [58]. Research indicates that traditional fermented beverages, when consumed in moderation, can offer a unique blend of probiotic benefits, bioactive compounds, and metabolic support, making them a lucrative part of functional food research, despite the well-documented health risks associated with excessive alcohol consumption. The market size of fermented alcoholic beverages is expected to grow at a CAGR of 10.74% from USD 2527 billion in 2024 to USD 5716.2 billion in 2032. The market is dominated largely by the Asia–Pacific region, with a market share of 40.44% in 2023, closely followed by the U.S.A.

Figure 1 broadly illustrates the representative fermented foods (category wise) from each region of the world along with the market leaders and shares.

Table 1. Global fermented foods, substrates used for fermentation, and their microbial composition, functional components, and health benefits.

Fermented Food	Substrate for Fermentation	Region	Microorganisms Used	Functional Components	Health Benefits	References
Vinegar	Alcoholic fermentation of fruit juice/grain mash followed by acetic acid fermentation	World-wide	Saccharomyces cerevisiae, Acetobacter aceti, Gluconobacter, and Komagataeibacter	Acetic acid, polyphenols, organic acids, amino acids, enzymes, minerals, and probiotics	Blood sugar regulation, antioxidant activity, digestion support, and antimicrobial effects	[59]
Dosa	Rice and black gram	India	Lactobacillus fermentum and Saccharomyces cerevisiae	Probiotic bacteria and organic acids	Supports digestion and improves nutrient absorption	[20]
Dawadawa	Locust beans	West Africa	Bacillus subtilis and Bacillus licheniformis	Peptides and antioxidants	Enhances protein digestibility and antimicrobial effects	[60]
Kinema	Soybeans	Nepal	Bacillus subtilis	Polyglutamic acid and isoflavones	Rich in bioactive peptides and supports digestion	[60]
Cheonggukjang	Soybeans	Korea	Bacillus subtilis	Polyglutamic acid and isoflavones	Anti-inflammatory and gut microbiota modulation	[60]
Kombucha	Sweetened tea	China and world-wide	Saccharomyces cerevisiae and Gluconacetobacter xylinus	Organic acids, polyphenols, and probiotic bacteria	Detoxification, gut health, and antioxidant	[61]
Amasi	Cow milk	Southern Africa	Lactococcus lactis and Leuconostoc mesenteroides	Organic acids and probiotic bacteria	Gut microbiota enhancement and immune support	[62]
Lassi	Fermented cow/buffalo milk	India	Lactobacillus spp.	Probiotic bacteria and organic acids	Enhances gut flora and cooling effect	[63]
Chhaang	Barley, millet, or rice	Nepal and Tibet	Wickerhamomyces anomalus	Polyphenols and organic acids	Antioxidant and supports gut microbiota	[55]
Poi	Corm of taro plant	Hawaii	Lactobacillus spp. and Geotrichum spp.	Organic acids and probiotic bacteria	Improves gut health and prebiotic properties	[64]
Sufu	Soybean curd	China and Taiwan	Actinomucor elegans and Rhizopus spp.	Isoflavones and peptides	Cardioprotective and antioxidant	[60]
Idli	Rice and black gram	India	Lactobacillus fermentum and Leuconostoc spp.	Probiotic bacteria and organic acids	Enhances digestibility and nutrient bioavailability	[20]
Puto	Rice flour	Philippines	Saccharomyces cerevisiae and Lactic acid bacteria	Probiotic bacteria and organic acids	Supports digestion and enhances nutrient uptake	[60]
Tofu	Dried soybeans	China and Japan	Lactobacillus spp. and Aspergillus spp.	Isoflavones and peptides	Cardioprotective and gut microbiota modulation	[65]
Garri	Cassava tubers	Nigeria	Lactobacillus plantarum and Saccharomyces spp.	Cyanide-reducing enzymes and organic acids	Detoxification and gut health	[66]
Tarhana	Yoghurt, flour, and vegetables	Turkey	Lactobacillus delbrueckii and Saccharomyces cerevisiae	Organic acids and probiotic bacteria	Enhances gut health and immune boosting	[67]
Kvarg (Quark)	Milk	Sweden	Lactococcus lactis and Streptococcus thermophilus	Probiotic bacteria and organic acids	Gut microbiota enhancement	[68]
Puto Bumbong	Glutinous rice, Pirurutong	Philippines	Saccharomyces cerevisiae	Probiotic bacteria and organic acids	Improves digestion and antioxidant	[69]
Tapai	Cassava or rice	Southeast Asia	Saccharomyces cerevisiae and Rhizopus spp.	Organic acids and probiotic bacteria	Enhances digestion and prebiotic benefits	[70]
Ayran	Yoghurt	Turkey	Lactobacillus bulgaricus and Streptococcus thermophilus	Probiotic bacteria and organic acids	Gut microbiota support and cooling effect	[71]
Togwa	Maize flour and finger millet	Tanzania	Lactobacillus plantarum and Saccharomyces cerevisiae	Organic acids and probiotic bacteria	Digestive support and immune enhancement	[72]
Buttermilk	Fermented milk	USA, Europe, and India	Lactococcus lactis and Leuconostoc spp.	Probiotic bacteria and lactic acid	Supports gut health and reduces cholesterol	[73]
Sour Cream	Fermented regular cream	USA and Europe	Lactococcus lactis and Streptococcus thermophilus	Probiotic bacteria and organic acids	Enhances digestion and gut microbiome support	[74]
Sourdough	Flour	Europe and USA	Lactobacillus sanfranciscensis and Saccharomyces cerevisiae	Organic acids and exopolysaccharides	Improves digestibility and supports gut microbiota	[75]
Clabber	Milk	Southern USA	Lactobacillus spp. and Streptococcus spp.	Probiotic bacteria and lactic acid	Enhances gut health and rich in probiotics	[76]
Shrikhand	Yoghurt	India	Lactobacillus spp.	Probiotic bacteria and lactic acid	Enhances digestion and rich in probiotics	[77]

specifically lists some of the fermented foods (not covered above) that are produced in different regions of the world, as well as the microbes and fermentation substrates, their functional properties, and their health advantages.

3. Omics Approach for Functional Food Development and Deciphering the Microbial Role in Fermentation

The previous section on traditional fermented foods and their associated microbes highlighted how mankind has long utilized microorganisms for fermentation. While traditional methods rely on empirical knowledge, modern advancements have revolutionized our understanding of the microbial interactions and metabolic pathways of the microorganisms involved in fermentation. Omics technologies provide deep insights into microbial diversity, functional roles, and metabolite production. These cutting-edge tools are paving the way for the development of innovative functional foods, enhanced food safety, and optimized fermentation processes. Until the popularity of advanced omics technologies, the specific processes controlling microbial interactions, metabolite production, and functional properties were not well understood. A comprehensive understanding of both microbial behaviour and fermented food properties is made possible by omics tools, which provide a revolutionary method for tracking down and describing traditional fermented foods. In general, there are two primary areas of omics research on fermented foods. The first uses a hierarchical framework of genomics, transcriptomics, proteomics, and metabolomics to study the behaviour of fermentation microorganisms and the mechanisms. The second component focuses on analyzing the properties of fermented food products, including their nutritional, sensory, functional, and safety attributes using metabolomics, peptidomics, and other cutting-edge omics techniques [78].

3.1. Types of Omics Utilized in Fermented Food

The various types of omics tools include genomics, transcriptomics, proteomics, metabolomics, macrogenomics, metaproteomics, and many more. Genomics deciphers microbial DNA sequences to unravel the genetic blueprint of fermenting organisms, enabling strain identification and functional gene characterization [79,80] (Figure 2a), while transcriptomics (Figure 2b) deals with gene expression patterns by analyzing RNA, revealing the metabolic responses and transcriptional regulation underlying fermentation processes [81]. Similarly, proteomics investigates the proteome, shedding light on the enzymes and proteins driving microbial metabolism and their interactions within the fermentation matrix [82] (Figure 2c), whereas metabolomics (Figure 2d) offers a holistic view of metabolic pathways and bioactive compounds, deciphering the biochemical transformations that shape the flavour, texture, and nutritional value of fermented foods [83]. On the other hand, macrogenomics extends genomic analysis to explore microbial diversity at a macro scale, elucidating ecological interactions and population dynamics in complex fermentation systems. By concentrating on the useful proteins found in microbial communities, metaproteomics makes it easier to link the presence of microorganisms to the results of fermentation. This is further expanded by peptidomics, which studies peptide fractions and reveals their bioactive characteristics, taste contributions, and health benefits. Similarly, lipidomics studies lipid changes, which are crucial for flavour development and the structural stability of some fermented products [84,85]. In order to capture strain-level diversity and reveal new functional genes essential for fermentation, metagenomics uses high-throughput sequencing to examine the collective genomes of microbial communities, further expanding the field of omics [79,80,86]. Although this makes thorough microbial profiling possible, there are drawbacks, including high expenses and a need for substantial data analysis. Figure 2a–d briefly illustrates the process flow of omics technology.

By monitoring the transcriptional activity of microbial genes in real time, metatranscriptomics enables the identification of metabolic adaptations and functional shifts in microbial populations. This method has proven to be very helpful in understanding the dynamic microbial reactions that occur during fermentation. Metaproteomics provides direct insights into microbial functionality within the fermentation ecosystem by characterizing proteins and their regulatory mechanisms, thereby bridging the gap between genetic potential and functional expression. The enormous genetic diversity found in microbial communities, however, makes it difficult to identify and quantify proteins. Last but not least, by analyzing small molecules and metabolic intermediates, as discussed earlier, metabolomics reveals important metabolic interactions, the production of bioactive compounds, and the fermentation-driven biochemical changes that impact a microbial system’s biochemical state. Combining metagenomics, metatranscriptomics, metaproteomics, and metabolomics, integrated multi-omics approaches are becoming crucial instruments for deciphering the molecular complexity of fermentation and enabling targeted enhancements in food quality, safety, and functionality [79,80,81,82,85,86,87,88].

3.2. Real-World Applications of Omics in Fermented Food

Several industrial applications have been successfully documented for omics in the fermented food industry. To incorporate omics data on fermentative microbes, an ‘Omics Database of Fermentative Microbes’ (ODFM) was created. For instance, to ensure food safety and sensory qualities, this database assists in evaluating the microbial strains for use as starter cultures. According to Lee et al. [89], it helps predict and regulate the fermentation of Kimchi. Similarly, microbes in pit mud and their impact on the flavour of Chinese strong flavour Baijiu were investigated using omics techniques. According to multi-omics data, specific bacterial communities had a major impact on the metabolism of organic acids, which in turn affected the final flavour [90]. Probiotic strains have been improved, and food microbial communities have been changed through the use of CRISPR-based genome editing in conjunction with omics technologies [91]. Figure 3a depicts the selection of starter cultures and improvement of strains for strain selection using genomics, CRISPR, and metagenomics. In another interesting study by Wu et al. [92], by adjusting the fermentation conditions, particularly lowering the pH to 5.5, influence was found on the metabolism of Streptococcus thermophilus ASCC1275. It enhanced arginine biosynthesis while reducing glutamate catabolism. Changes in the metabolic pathways impacting the production of exopolysaccharides (EPSs), which are essential for the texture and functionality of fermented dairy products, were discovered using metaproteomics and metatranscriptomics analyses (Figure 3b). To exemplify the functionality of fermented foods, several omics have been used. In a recent work, Astragalus, which was fermented using Bacillus subtilis, was tested in a mouse model for hyperuricemia. As per the multi-omics data, fermentation reduced kidney inflammation and regulated uric acid transporters by increasing the amount of beneficial bacteria such as Lactobacillus enterocolitica and Odoribacter splanchnicus [93]. Apart from the above, other applications include the development of flavour in fermented foods with the help of omics. For example, 130 upregulated metabolites and 160 downregulated proteins associated with soybean fermentation flavours were discovered using transcriptomics, proteomics, and metabolomics [94]. As per the multi-omics data, the main bacteria that produce 47.7% of the ketones and alcohols in cheese and influence its final aroma are Pseudoalteromonas and Marinomonas [95]. In another work by Hu et al. [96], with the aid of genomics and metabolomics research, it was found that Aspergillus fungi produce hydrolases that break down the cell walls of tea, releasing soluble carbohydrates and amino acids that enhance taste (Figure 3c).

Omics technologies have also been extensively applied in ensuring quality control and food safety in fermented food systems. According to a study, the distinct ingredients of Kimchi and their effects on microbial fermentation were studied with help of multi–omics. The ingredients led to differences in the dominant microbes and their niche, which affected the success of fermentation [97]. Omics techniques were used to analyze bacterial diversity in another study by Medina et al. [98] on the fermentation of table olives. A total of 131 bacterial genera were found using high-throughput sequencing, which also showed microbial changes over a 120-day period. While halophilic bacteria and spoilage microorganisms continued to exist, Celerinatantimonas eventually took over, along with spoilage microorganisms, Pseudomonas, and Propionibacterium. The results demonstrate ‘how’ omics can be used to better understand fermentation microbiota and enhance quality control (Figure 3d).

Omics technologies are therefore essential tools in contemporary food biotechnology, because they offer a strong framework for improving the quality of fermentation, guaranteeing safety, and maximizing microbial interactions. Figure 3 illustrates the above-cited important applications of omics and multi-omics in the fermented food industry.

Table 2. Recent successful applications of various omics and multi-omics in the food fermentation industry.

Omics Technique	Microorganism Used	Applications in Food Fermentation Industry	References
Metagenomics and metatranscriptomics	Providencia stuartii	To understand the metabolic potential and microbial community structure of fermented soybeans	[81]
Transcriptomics	Aspergillus oryzae	To analyze the gene expression related to enzyme production in Koji (Soy Sauce) fermentation	[99]
Multi-omics	Bacillus subtilis BJ3-2	To investigate the fermentative strains to gain a better understanding of soybean flavour compounds and Soy Sauce-like flavor formation	[94]
Metatranscriptomics	Lactobacillus Tetragenococcus	To investigate the role of microorganisms in the flavour development of Dajiang during fermentation	[87]
Metagenomics and metabolomics	Moulds and bacteria	To confirm the microbes impacted by the variations in ripening techniques and to elucidate the relationship between the metabolites and microbiota of cheese ripened by surface mould and cheese ripened by bacterial smear	[95]
Proteomics	Methanobacterium spp. and Clostridium spp.	To compare the levels of protein expression in the 30- and 300-year pit muds of Luzhou flavour liquor	[100]
Metabolomics	Lactobacillus plantarum	To monitor the citric acid quantity in batch fermentation for production of Kimchi	[86]
Metabolomics and proteomics	Mixed fungi and Aspergillus spp.	To assess the change in mechanisms of non-volatile compounds during the white tea (Camellia sinensis) fermentation process	[82]
Transcriptomics	Chromohalobacter, Halomonas, Marinobacter, Debaryomyces, and Wickerhamomyces	To explore role of microorganisms in the development of the flavour and taste of fermented gajang (Soy Sauce)	[101]
Genomics, proteomics, and metabolomics	Saccharomyces cerevisiae and Oenococcus oeni.	To investigate the relationships between microbial communities and the factory environment during wine fermentation	[102]

enlists some of the recent examples of successful applications of omics and multi-omics in the food fermentation industry.

3.3. Single-Omics or Multi-Omics: Which One Is More Effective?

In food fermentation, the effectiveness of single-omics and multi-omics approaches in yielding useful insights is at the centre of confusion. Even though individual omics methods, like metabolomics or genomics, provide useful information by focusing on a different facet of microbial function, they only offer fragmented insights into the complexity of fermentation processes. They often only give a partial picture of the dynamics of microbes and metabolism. In contrast, multi-omics methods combine several levels of biological data to produce a more thorough comprehension of fermentation processes by integrating genomics, transcriptomics, proteomics, and metabolomics data [15,88]. The synthesis of bioactive compounds, metabolic fluxes, and microbial interactions have all been found to be more accurately identified via multi-omics techniques. Researchers link genetic potential to metabolic outcomes and functional expression of genes by integrating all single omics. For example, the identification of important microbial players involved in the development of flavour and texture in traditional fermented foods has improved as a result of the integration of metagenomics and metabolomics. However, compared to single-omics studies, multi-omics approaches are more complex and require sophisticated computational tools, data integration pipelines, and substantial financial investment. Therefore, multi-omics approaches offer a comprehensive perspective that improves strain selection, process optimization, and product innovation in food fermentation, even though single-omics techniques are still helpful for focused research [84,103].

4. Advancing the Role of Precision Fermentation in Food Fermentation and Microbial Functionality

Precision fermentation is a cutting-edge biotechnology method that uses microorganisms to sustainably produce food. It enhances the microbial biosynthesis of food molecules like proteins, lipids, flavours, pigments, and vitamins from abundant, low-cost substrates by combining metabolic engineering and synthetic biology. In order to improve the texture, flavour, and nutritional qualities of food products, this method introduces or modifies metabolic pathways in generally recognized as safe (GRAS) microorganisms. It also maximizes yield, efficiency, and product functionality. To achieve this, scientists modify the genes of microorganisms, which then carry out fermentation using the provided nutrients, producing the desired compound, which is later extracted [11,104].

A stakeholder roundtable meeting was held in November 2023 in Shanghai, China by the Food and Agriculture Organization (FAO) to address advancements in precision fermentation products and cell-based foods, along with related food safety issues. Collagen, enzymes, myoglobin, cell-based deer antlers, cell-based foie gras, cell-cultured bluefin tuna, cell-based beef, cell-based wagyu beef, cell-based milk lipids, and cell-based pork products were among the many cell-based and precision fermentation products that were discussed at the meeting. The FAO acknowledged precision fermentation as a crucial advancement in food production, highlighting its potential to improve nutritional profiles, mitigate environmental impacts, and address issues related to food security. According to the FAO report, precision fermentation has the potential to revolutionize food supply chains by generating proteins and nutrients separately from traditional agriculture, thereby reducing the effects of climate change and resource depletion. It also highlighted how developments in precision fermentation can lessen the dependency on resource-intensive farming methods and animal agriculture, while helping to meet the world’s expanding protein needs. Apart from this, it was also stated by the FAO that precision fermentation may be a key factor in repurposing food waste and excess biomass into products with added value. Making use of non-food-based feedstocks is consistent with the circular bioeconomy model, which guarantees less dependence on limited resources while safeguarding the resilience of the food system. Therefore, increasing the use of precision fermentation in food production could improve food security worldwide by establishing more resilient and localized food supply chains [105].

Microbial hosts like Saccharomyces cerevisiae, Escherichia coli, Aspergillus niger, and Pichia pastoris are used in precision fermentation to achieve a specific biosynthesis. Adaptive evolution and strain selection for maximum production efficiency, the deletion of competitive pathways to increase metabolic flux towards desired products, and the insertion of heterologous genes for novel protein and enzyme synthesis are all made possible by genetic modifications, such as CRISPR-Cas9 and recombinant DNA technology [106]. Additionally, recent developments in synthetic biology have brought forth chassis microorganisms that are specifically engineered for the production of high-yield proteins and metabolites. The stability and increased biosynthetic efficiency of these engineered microbes guarantee reliable industrial-scale applications [107]. Also, the efficiency of fermentation is greatly influenced by the substrate selection. By maximizing the use of abundant, affordable feedstocks like lignocellulosic hydrolysates and agricultural by-products, precision fermentation improves sustainability and economic viability. To optimize microbial productivity, process variables such as oxygen transfer, pH regulation, and bioreactor design are adjusted [108].

4.1. Applications of Precision Fermentation in the Food Industry

The rising significance of precision fermentation is a note-worthy development for utilizing the functional properties of microorganisms in the food industry. Several applications of precision fermentation have been documented across the world. For example, the flavour enhancement of fermented foods is one important application of precision fermentation. Researchers have been able to directly alter flavour profiles by introducing heterologous genes or altering endogenous pathways in food-fermenting microorganisms such as Lactococcus lactis and Saccharomyces cerevisiae [109]. To improve the aroma of tropical fruit in wine, Holt et al., for instance, modified S. cerevisiae to overexpress the genes involved in the synthesis of volatile thiols [110]. Similarly to this, Denby et al. created a genetically modified brewing yeast that can produce the essential flavour components of hops, allowing for the creation of hoppy beers without the use of hops [111]. Figure 4a depicts the role of precision fermentation in flavour enhancement.

Precision fermentation also has the potential to improve food safety in addition to flavour. Antimicrobial compounds such as bacteriocins and endolysins, which prevent the growth of foodborne pathogens, are produced by microbes that have been genetically modified [112]. The use of genetic engineering to enhance the activity of nisin, a common bacteriocin in food preservation, was reviewed by Zhang et al. [113]. Additionally, microbes have been altered to decrease the production of harmful compounds like acrylamide in baked and fried foods [113]. Figure 4b summarizes the role of precision fermentation in food safety. Beyond flavour and safety applications, precision fermentation has made it possible to produce functional food ingredients in a sustainable way. As an alternative to resource-intensive animal-based production, researchers have engineered GRAS fungi, such as Trichoderma reesei and Aspergillus oryzae, to heterologously express animal proteins, such as dairy and egg proteins [114]. Figure 4c depicts the role of precision fermentation in producing functional food ingredients. Perfect Day, ImaginDairy, and The EVERY Company are leading the way in using precision fermentation to produce animal-free functional food ingredients.

Other major potential applications include the production of collagen, a protein with various food industry applications like improving nutrition, texture, solubility, and functionality [115]. The manufacturing process involves high-density microbial fermentation, followed by downstream processing to extract and purify the collagen. This approach can minimize the use of animals and reduce environmental impact compared to conventional collagen sources. Likewise, myoglobin, a protein that provides the red colour and flavour in meat, can be produced through precision fermentation using genetically modified yeast strains [116,117]. The resulting myoglobin-based ingredient, marketed as TAMEE, has the same amino acid sequence and properties as native bovine myoglobin, making it a potential meat alternative. Apart from proteins, precision fermentation can also be used to produce enzymes like xylanase, which are used as food ingredients to enhance the quality of baked goods [105]. The production process involves an enzyme discovery cycle that combines in silico, in vitro, and in pan approaches to identify and optimize the production of target enzymes. Ensuring the safety and purity of the final enzyme product is critical [104,107]. Figure 4d signifies the role of precision fermentation in the production of alternative proteins.

Therefore, precision fermentation aids in the production of alternative proteins (e.g., casein, whey, myoglobin, and hemoglobin) for plant-based dairy and meat substitutes, vitamins, and bioactives (e.g., vitamin B12, omega-3, and antioxidants) to enhance nutritional value, flavours, and texturizers (e.g., vanillin, umami peptides, and polysaccharides) and improve sensory attributes and functional enzymes (e.g., chymosin, amylase, and pectinase) for food processing efficiency [11].

4.2. Impact of Precision Fermentation on Various Aspects of the Food Industry

Precision fermentation is transforming the food industry by enabling the sustainable production of high-quality ingredients [118], reducing environmental impact, enhancing food security, and decreasing reliance on animal agriculture. By using microorganisms to produce target compounds [114], precision fermentation is reducing the reliance on animal-derived sources and minimizing the environmental footprint associated with conventional production methods. It is also expanding the diversity of sustainable protein and nutrient sources [107], contributing to improved global food security and nutrition [116]. The ability to customize growth media and production conditions allows for the development of novel food ingredients and products tailored to specific consumer preferences and nutritional needs, propelled by precision fermentation. This technique’s products can undergo rigorous safety assessments, including evaluations of genetic stability, microbiological safety, and potential allergenicity, to ensure their suitability for human consumption. Also, precision fermentation offers significant advantages over traditional food production, such as reduced reliance on animal agriculture and lowering greenhouse gas emissions and land use, hence promoting sustainability [109]. It enables the upcycling of food waste into valuable bioproducts [119]. Such advances in bioprocess engineering improve TRY (titer, rate, yield), making commercial applications feasible [11]. Overall, precision fermentation is a rapidly evolving field that holds promise for addressing various challenges in the food and agriculture sector, from improving sustainability to expanding the diversity of safe and nutritious food options.

5. Role of Artificial Intelligence and Machine Learning in Food Fermentation

Traditional fermented foods can be studied with great effectiveness using AI and ML techniques. Research on fermented foods has seen an increase in bioinformatics data, which calls for more sophisticated methods that can manage complex and high-dimensional data. As a science that mimics and expands human intelligence, AI is a vital component of contemporary computational technologies and optimization algorithms. AI tools are being used to monitor and optimize important production chain control points and to customize products for consumers. A Japanese sake maker, for example, has developed a computer vision-based AI tool that uses image data analysis to figure out when it is best to drain rice before steaming [120]. In this, a predictive AI model optimizing the sake brewing process has been created by combining equipment learning and the mathematical modelling of the brewing process (Figure 5a). In another study by Zhu et al. [121], an investigation was conducted on how ML algorithms can guarantee quality control in black tea fermentation. The Leading Capacitance and Resistance (LCR) metre was used in the study to measure 11 electrical parameters of tea leaves, offering a non-destructive way to track the fermentation process in real time. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) were used to objectively classify tea samples, enabling differentiation based on differences in pigment composition and catechin content. Additionally, to estimate the degree of fermentation, predictive models using support vector machines (SVMs), random forests (RFs), and multilayer perceptron (MLP) were created. These models allowed for the accurate classification and evaluation of the fermentation stages by using electrical property data as input variables and the HCA clustering results as reference outputs (Figure 5b). By maximizing the umami balance and nutritional composition while reducing waste, machine learning models help fermented sauces like Ganjang (soy sauce) and Doenjang (soybean paste) to age even better [122] (Figure 5c). Additionally, in a fermentation study on Kombucha, Zhao et al. [123] explored how digital twin (DT) technology can be used to optimize Kombucha fermentation through process control, predictive modelling, and real-time monitoring (Figure 5d). Key fermentation parameters, such as the bacterial concentration, carbon source concentration, total acid, pH, dissolved oxygen, and L-theanine, were continuously monitored using an IoT-based system. With the help of these data, partial least squares (PLSs) regression models were trained to accurately predict the concentrations of carbon sources and bacteria. A multi-scale convolutional filter was created for effective feature extraction and fusion in order to improve model performance, which greatly increased prediction accuracy. With ratio of performance to deviation (RPD) values of 5.63 and 6.52 and root mean square error of prediction (RMSEP) values of 0.5538 mg/mL and 0.0558 (Au), the convolution fusion-based PLS model showed strong predictive abilities. Also, to dynamically control the fermentation conditions, an AI-driven optimal control system incorporating genetic algorithms (GAs) was built. According to the simulation results, this DT-based strategy successfully adjusted variables like the pH and dissolved oxygen, which enhanced bacterial growth and carbon source utilization and raised fermentation efficiency. Simultaneously, Dongre and Patel [122] demonstrated the real-time monitoring of fermentation parameters like the temperature, pH, humidity, and microbial activity in the production of Kimchi using AI-powered sensors and IoT devices (Figure 5e). This allows for automated adjustments to maintain the ideal conditions and guarantee consistent product quality. Predictive analytics powered by AI also assists producers in matching fermented food items to changing consumer tastes, which makes it easier to create plant-based or low-sodium substitutes for traditional Korean dishes. AI improves efficiency and consistency in Makgeolli (Korean rice wine) production [122] by precisely regulating the alcohol concentration and aroma, which optimizes fermentation. In another innovative work [124], the spatiotemporal evolution of two interacting microorganisms was simulated using image data. Deep neural network models were then trained to accurately predict microbial interactions under various culture conditions. These advanced techniques are able to predict microbial strain growth conditions and even the interactions between strains with high accuracy (Figure 5f).

Therefore, by citing various recent examples, it has been proven that AI is revolutionizing traditional fermentation techniques for better quality, scalability, and consumer-driven innovation in the fermented food industry. Also, AI technologies are playing a crucial role in precision fermentation by enabling real-time monitoring, process optimization, and quality control. Through ML models and computer vision, fermentation processes such as sake brewing and tea fermentation are made more efficient and consistent. These advances help to maximize product quality while reducing waste and improving scalability. They are also improving process efficiency, guaranteeing product consistency, permitting real-time monitoring, and facilitating predictive optimization.

6. Current Challenges Faced by the Fermented Food Industry

Numerous obstacles encompassing the microbial, technological, regulatory, environmental, and economic domains hinder the fermented food industry. One of the biggest problems is managing microbial activity, where choosing the right microbial strains with the right fermentation properties is crucial in creating reliable and efficient starter cultures. The quality, safety, and sensory qualities of fermented products can be severely compromised by the unpredictable possibility of contamination by pathogens or spoilage microorganisms and variations in microbial performance. Since enzymes are essential for the breakdown of complex molecules and affect the final product’s texture, flavour, and nutritional profile, managing enzymatic activity in fermentation processes is equally difficult. However, under changing environmental conditions, enzymes derived from various microbial strains may show varying activity, resulting in inconsistent product characteristics [125].

Managing the temperature, acidity, dissolved oxygen, redox potential, and fermentation duration precisely is yet another significant challenge. To achieve the desired biochemical changes and functional qualities of the product, it is essential to keep these parameters within the ideal ranges. Traditional fermentation methods, on the other hand, frequently lack the technological advancements required to precisely control these variables, which results in less than desired yields, uneven textures, and variable flavour profiles. In order to maintain consistency and efficiency during the shift from small-scale artisanal production to large-scale industrial manufacturing, strict quality control, ongoing process optimization, and technological advancements are necessary. These challenges become worse when the fermentation process is scaled up. Additionally, large-scale operations require large investments in sophisticated bioreactors, automated monitoring systems, and specialized equipment, making expansion economically unfeasible [124].

Another significant challenge is regulatory compliance, since the production of fermented foods should meet strict safety regulations while preserving cost-effectiveness and production efficiency. Manufacturers’ ability to experiment with new ingredients and creative methods is often restricted by regulations that place stringent controls on microbial starter cultures, ingredient sourcing, and fermentation processes [124]. This complexity is increased by the fact that food safety laws are always changing, necessitating that businesses adjust to new testing procedures, microbial inactivation verification, and compliance requirements. This raises production costs and operational complexity considerably by requiring investments in specialized laboratories, environmental sampling programmes, and microbiological expertise. The commercial potential of many functional fermented foods is also limited by the absence of standardized international legislation regarding probiotic and fermented food health claims. This is because regulatory bodies require substantial scientific evidence before approving marketing claims related to health. For example, only one of the more than four-hundred health claim applications for probiotics and fermented foods has been accepted by the European Commission, underscoring the regulatory obstacles that prevent market growth [126].

Environmental sustainability is one of the most urgent issues lurking over the fermented food sector. In order to prevent climate change and maintain ecological sustainability, fermented food production, especially on an industrial scale, must adhere to environmental regulations. Food shortages and environmental degradation are made worse by the significant amounts of agricultural produce that are lost or wasted during food processing as a result of inefficiencies, poor storage, and a lack of preservation techniques. Because their disposal necessitates careful management to prevent pollution and resource waste, fermentation by-products and waste streams also contribute to environmental concerns. The sector must also overcome the obstacles of cutting its carbon footprint, making the best use of its resources, and creating sustainable fermentation methods that support international environmental goals [127].

The fermented food industry is further complicated by changes in consumer health preferences. A rise in metabolic disorders like obesity, Type 2 diabetes, cardiovascular diseases, and neurodegenerative conditions has been attributed to modern dietary and lifestyle habits that include the excessive consumption of refined carbohydrates, sugars, processed meats, artificial additives, and trans fats. As a result, consumers are calling for more fermented foods that provide functional health benefits like improved gut microbiota support, increased probiotic activity, and improved nutrient bioavailability. However, creating such products while adhering to legal requirements and environment sustainability and guaranteeing microbial stability is a difficult task. Additionally, the need for preservatives to maintain microbial stability and a longer shelf life frequently runs counter to consumer preferences for natural, clean-label, and minimally processed foods [128].

Regional differences in production methods, especially in developing nations where food processing is still very nascent and dispersed, add on to the challenges being faced by the fermented food sector. Significant risks of microbiological contamination are caused by inadequate quality control procedures, inadequate supervisory systems, and a lack of awareness among food handlers. The risk of pathogen contamination, which can result in foodborne illnesses and compromised product safety, is further increased by the use of low-quality raw ingredients, inadequate hygiene practices, poor storage conditions, and limited access to clean water sources. These elements emphasize the necessity of stricter quality control procedures, better food safety guidelines, and upgraded facilities to support the expansion of the fermentation sector in developing nations [129].

7. Mitigation Strategies and Future Prospects

The food fermentation sector needs to take a diversified approach that incorporates sustainability programmes, legal compliances, and technological developments in order to overcome the previously discussed obstacles. This will not only increase the market share of underdeveloped nations in terms of fermented food production but also boost their economy through export. For this, utilizing cutting-edge fermentation methods and biotechnological advancements is one important remedy. Optimized microbial enzymes, precision fermentation, and advanced starter cultures can all improve the effectiveness and productivity of fermentation processes. Digital twin (DT) technology, automation, and real-time monitoring can all be used to precisely control fermentation parameters, guaranteeing consistent product quality and lowering the risk of microbial contamination. For example, the real-time monitoring of fermentation parameters like carbon source consumption, temperature, pH, humidity, dissolved oxygen levels, organic acid production, and microbial activity is made possible by AI-powered sensors and IoT devices. By predicting and correcting variations in the required parameters, these systems can guarantee a constant level of quality in fermented food like Soy Sauce and Kimchi. Similarly, predictive analytics powered by AI can also be extremely crucial for enhancing product development and fermentation process optimization. These data-driven methods make it easier to create predictive models that optimize fermentation processes and increase yield efficiency by utilizing ML techniques like multi-scale convolutional filtering and PLS regression. To preserve flavour balance and nutritional value, ML models can be used to categorize fermentation stages, forecast enzymatic activity, and optimize ageing procedures. By modifying fermentation conditions in real time, AI algorithms can control the alcohol concentration and aroma in the production of traditional fermented beverages like Makgeolli. Additionally, by examining consumer trends and preferences, AI can support consumer-driven product development, resulting in innovations like low-sodium fermented foods or plant-based foods that are suited to particular dietary requirements. Lastly, a revolutionary method for optimizing the fermentation process is provided by the combination of AI and DT. AI-driven systems can improve fermentation processes’ efficiency and reproducibility by facilitating automated control, predictive modelling, and real-time monitoring. The development of AI-powered software for reconstructing metabolic models and optimizing microbial interactions will further accelerate advancements in the field. Adopting AI and precision fermentation will be essential as the sector develops, to meet present issues and open up fresh avenues for creativity, sustainability, and health promotion.

Advanced microbial selection methods, such as metagenomics and bioinformatics (omics and multi-omics), can increase the stability of starter cultures, lower the risk of contamination, and boost fermentation efficiency in addition to AI and ML. It is very promising to create new fermented foods with improved health benefits through precision fermentation, which uses genetically modified microorganisms to produce particular functional compounds. Furthermore, precise biochemical transformations can be achieved by incorporating controlled enzymatic reactions using engineered enzymes with known specific activities. This enhances the nutritional profile, texture, and taste of fermented foods. Another exciting area for future study is the incorporation of AI into metabolic network modelling. A greater comprehension of microbial interactions in fermented foods can be made possible by the high accuracy with which AI-powered tools can reconstruct genome-scale community metabolic models (GSCMMs). Research in microbial ecology and the development of functional foods can be accelerated by using ML-based training on complex conditional constraints to increase model precision and enable real-time predictions. Additionally, high-dimensional data from fermentation studies can be managed by AI-based bioinformatics platforms, which can help identify new microbial strains and fermentation pathways.

In order to guarantee sustainability, the fermented food industry must investigate waste valorization techniques by turning food processing by-products into value-added products. Similarly, in order to support circular economy initiatives, fermentation can be used to convert agricultural waste into bioactive compounds, pigments, enzymes, and even biofuels. By combining contemporary quality control methods with traditional fermentation knowledge, small-scale producers and artisanal fermenters also have a great chance to spur innovation in the industry. Local and sustainable food production can be promoted by regional producers working together to optimize resources and share knowledge. Additionally, regulatory frameworks need to change to reflect the increasing complexity of producing fermented foods. Clarity for both producers and consumers can be achieved by creating standardized guidelines for probiotic and fermented food health claims. Strict adherence to Hazard Analysis and Critical Control Points (HACCPs) and Good Manufacturing Practices (GMPs) can reduce contamination risks and improve microbiological safety. Furthermore, more funding for education and research can increase the knowledge of the advantages of fermentation and encourage the industry as a whole to adopt the best practices.

Therefore, the combination of contemporary scientific discoveries and traditional fermentation knowledge will determine the direction of the fermented food sector in the future. The next wave of innovation in the sector will be driven by the use of omics technologies, precision fermentation, AI-driven fermentation control, and sustainable production methods. Enhancing bioprocess automation, creating standardized regulatory frameworks for innovative fermented products, and improving AI-based metabolic network modelling should be the main areas of future research. The industry can overcome its current obstacles and open up new avenues for the production of fermented foods that are economically viable, environmentally friendly, and health conscious by utilizing digitalization, technological advancements, and regulatory harmonization. The food fermentation industry can establish itself as a major force in environmental sustainability, nutrition improvement, and global food security by investing more in research, technology, and consumer education.

8. Conclusions

Human civilization has relied extensively on fermentation to preserve food, increase its nutritional value, and create unique sensory attributes that characterize traditional cuisines worldwide, as already discussed in this study. It has also been observed that established categories of fermented foods maintain a significant share of the global market, with North America, Europe, and China emerging as the dominant contributors to production and consumption. As our understanding of food fermentation grows, from this study, it has been proven how traditional fermentation techniques are starting to be revolutionized via contemporary biotechnological tools. Comprehensive information about microbial communities, their metabolic processes, and their interactions within the fermentation matrix can be obtained through omics technologies. As an extension of these developments, precision fermentation utilizes metabolic engineering and synthetic biology to create highly specific functional ingredients. This ensures safety, effectiveness, and reproducibility while enabling the enhancement of fermented foods with specific health benefits. Another major leap in food fermentation is the integration of AI and ML. There are now more opportunities to create intelligent fermentation systems thanks to AI-driven methods in microbial modelling, process optimization, and quality control. Especially in large-scale industrial fermentation, computational modelling and AI-driven feature extraction techniques help to improve product consistency, refine fermentation kinetics, and guarantee quality assurance. The fermented food industry still faces a number of urgent issues in spite of these impressive developments, as discussed in Section 6, with mitigation strategies and future prospects in Section 7. This study emphasizes the many facets of fermentation, from its historical roots to its contemporary uses and market analysis. It specifically focuses on the latest biotechnological advancements in the form of omics, precision fermentation, and AI. By connecting traditional knowledge with State-of-the-Art scientific discoveries, it offers a thorough examination of how fermentation science is developing to satisfy contemporary needs for food security, sustainability, and nutrition. The future of global food systems can be greatly influenced by food fermentation, which is at the vanguard of a revolutionary era marked by the ongoing convergence of microbial ecology, biotechnology, and AI-driven analytics.